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HuTaoJiaZiAckerman avatar HuTaoJiaZiAckerman commented on August 23, 2024 1

Can you try that your tree.nek file put on itol(https://itol.embl.de/) websites to re-root. After export again as a nwk format, you code will work! I hope this approach can slove the problem.

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millanek avatar millanek commented on August 23, 2024

Hi Mike
My best guess would be a spelling error in your tree file. If you can't figure it out, feel free to email me with your combined_tree.txt and the tree.nwk files, I can try to investigate.

Kind regards
Milan

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mrml500 avatar mrml500 commented on August 23, 2024

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millanek avatar millanek commented on August 23, 2024

Hi Mike

Thanks for your patience. A few other people reported similar problems. The reason is: Dtrios just kind of "looks over” the tree to find the arrangement of the trios, whereas Fbranch needs to do a full tree data-structure parsing. So the code is different, and the Fbranch code was less flexible about the format of the input. In your case it was the dashes "-" in the taxon names that caused the trouble.

I have made the parser more flexible, so I think it should work with your file and also for people who have blank spaces in the group names. I also added a check for duplicate entries in the trees. This is all in the latest version r38.

Milan

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siberianhigh avatar siberianhigh commented on August 23, 2024

Hi Milan,

I've got the same problem with the version 0.4 r38

Dsuite Fbranch tree.txt sets__tree.txt > fbranch.txt ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: (Outgroup,internalNode1X,internalNode5X);

But my tree is very simple: (Outgroup,((a,b),c),(((d,h),(e,f)),g));

Do you have any suggestions?

best,
Evgeniy

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SethMusker avatar SethMusker commented on August 23, 2024

I had a problem with full stops (periods) in my names as well. Replacing with underscores fixed the problem.

@siberianhigh Try putting the outgroup at the end?
(((a,b),c),(((d,h),(e,f)),g),Outgroup);

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furr-rui avatar furr-rui commented on August 23, 2024

Hi Milan,

I've got the same problem with the version 0.4 r38

Dsuite Fbranch all10qa11qv.nwk out_combined_tree.txt > all10pop_branch.txt
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is:
(((((((internalNode0X,(internalNode1X)),TBS),internalNode4X),JJL),DWX),internalNode13X),Outgroup);
Do you have any suggestions?

best,
frr

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SethMusker avatar SethMusker commented on August 23, 2024

It looks like the brackets around (internalNode1X) might be redundant. Try removing them?

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furr-rui avatar furr-rui commented on August 23, 2024

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yefanglee avatar yefanglee commented on August 23, 2024

Thank you for your reply. I have successfully solved this problem.

------------------ 原始邮件 ------------------ 发件人: "millanek/Dsuite" @.>; 发送时间: 2022年1月12日(星期三) 下午4:16 @.>; @.@.>; 主题: Re: [millanek/Dsuite] Error when parsing tree with Fbranch (#22) It looks like the brackets around (internalNode1X) might be redundant. Try removing them? — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: @.***>

Hi, I met the same problems as you. Could you please tell me how to solve it? Thanks!
((((((internalNode0X)))),(internalNode1X,((NUB),((SIB))))),((FAL.00099760),((BEZ),((WAS,((EUR),((SAF),(EAF,(NAF))))),((SAS),(SC,(NC)))))))

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Prashantevo avatar Prashantevo commented on August 23, 2024

Hi there,

I am having the same error as above.

ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is:
((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);

I do not have any pop name with periods or - , rather 1pop, 2pop.

I also tried with new version yet getting same issue. Can someone help ?

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yefanglee avatar yefanglee commented on August 23, 2024

Hi there,

I am having the same error as above.

ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: ((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);

I do not have any pop name with periods or - , rather 1pop, 2pop.

I also tried with new version yet getting same issue. Can someone help ?

that means your tree string was not correct. you can check carefully tree string.

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Prashantevo avatar Prashantevo commented on August 23, 2024

Hi there,
I am having the same error as above.
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: ((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);
I do not have any pop name with periods or - , rather 1pop, 2pop.
I also tried with new version yet getting same issue. Can someone help ?

that means your tree string was not correct. you can check carefully tree string.

I used the tree generated by FastTree just removing branch values.

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yefanglee avatar yefanglee commented on August 23, 2024

Hi there,
I am having the same error as above.
ERROR: The tree string could not be parsed correctly! The remaining unparsed tree string is: ((Dpop,(internalNode1X,internalNode7X,(11pop,internalNode8X,internalNode11X))),Outgroup);
I do not have any pop name with periods or - , rather 1pop, 2pop.
I also tried with new version yet getting same issue. Can someone help ?

that means your tree string was not correct. you can check carefully tree string.

I used the tree generated by FastTree just removing branch values.

So did I, but the tree string generated by FastTree always didn't work for branch. I conducted a NWK file by myself.

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Prashantevo avatar Prashantevo commented on August 23, 2024

Thank you so much for your reply.

I am confused how would you revise/edit tree.
my tree looks like this:

(Outgroup,(18pop,((15pop,(17pop,16pop)),(7pop,(6pop,(5pop,(4pop,(3pop,(1pop,2pop)))))),((11pop,(8pop,10pop),((12pop,9pop),(14pop,13pop)))))));

PS: I have also tried putting outgroup at the end

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yefanglee avatar yefanglee commented on August 23, 2024

Thank you so much for your reply.

I am confused how would you revise/edit tree. my tree looks like this:

(Outgroup,(18pop,((15pop,(17pop,16pop)),(7pop,(6pop,(5pop,(4pop,(3pop,(1pop,2pop)))))),((11pop,(8pop,10pop),((12pop,9pop),(14pop,13pop)))))));

PS: I have also tried putting outgroup at the end

your original tree was showed in below according to your tree string. But I think there was something wrong with it.
image
Here I reconstructed a tree string: (((((((((((1,2),3),4),5),6),7),((((9,12),(13,14)),(8,10)),11)),((16,17),15)),19),O). I am not sure if it can success in Franch.

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Prashantevo avatar Prashantevo commented on August 23, 2024

Thank you very much. I removed 19 and it worked.

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